After upgrading to 13.8.1, any of these renders which were already sitting in AE, or if I freshly imported them, would change colour. Hard to tell what is exactly happening but a lot of the colours are getting replaced with reds. Checking them in quicktime player or premier they looked fine. It is just the latest version of AE that is doing this for some reason.

We suspect that there is some cached data that causes the new native QuickTime PNG decoder to misinterpret the alpha channel. Please reply as to whether or not the steps from that thread clear the problem.